Fitting Data to Darwinism Takes Creativity and Spin

Fairly regularly, papers appear in journals under the heading of Evolution.  The ones dealing with genetics tend to be hard to follow.  They are filled with jargon, correlation scores, charts and network diagrams.  They employ algorithms and databases unfamiliar to the lay reader.  Overall, though, they claim to find support for Darwin’s tree of life in the genes or metabolic networks of this or that group of organisms.  Does Darwinism pop right out of the data, or does it take some massaging to make Darwin fit the observations?  Let’s take one example that appeared in PNAS today for a look inside the engine room of how evidential support for evolution is manufactured.¹
    Kreimer et al set out to find the “evolution of modularity in bacterial metabolic networks.”  What they were looking for, in other words, is whether the amount of modularity in the ways proteins interact follows their assumed evolutionary relationships.  What is modularity?  That had to be defined in the Materials & Methods section.  First, they had to assign network scores to proteins based on what other proteins they interact with.  In the process, they tossed out water, protons and electrons.  Why?  Because someone else in the references did so – who had also written a paper on “The effect of oxygen on biochemical networks and the evolution of complex life.”  Already there seems to be some circularity in the reasoning.
    Next, they had to assign “modularity” values to the networks.  (This refers roughly to the degree a network of interacting proteins could be isolated from other networks.)  To do this, they used Newman’s algorithm, but they purposely avoided using an algorithm from another paper on the evolution of network modularity.  The authors could probably justify these choices, but they were clearly making human judgment calls on what algorithms would produce meaningful results.
    Once they had modularity scores, they had to decide how to measure environmental influences on various bacteria species.  They used the number of transporter genes found in databases as a proxy for environmental diversity; however, the paper admits that “the large scale KEGG data [Kyoto Encyclopedia of Genes and Genomes] used is not free from noise and missing information, and the representation used lacks reactions’ directionality, stoichiometry and more.”  That word “more” sounds worrisome.  How can they know they have meaningful data?  Their reassurance was only general: “However, the large scope of the data used permits a very large-scale investigation across hundreds of networks and leads to the identification of general relations that run across the data.”  OK, we’ll take their word for it.  The worries do not stop there, though.
    Next they had to figure out the phylogenetic tree of their bacteria.  Here they just borrowed one from another paper in the references.  One might think this is odd, since the goal of the paper was to show evolution, not to assume it:

The tree of life generated in ref. 21 was used to identify the phylogenetic relations between the species studied in our analysis and for inferring ancestral metabolic networks along the tree.  This tree includes a relatively large number of species, covering most of the taxonomic groups for which metabolic data are available.  Specifically, this tree was used to measure the distance of each extant and ancestral species to the last universal common ancestors of bacteria and to calculate the species pairwise phylogenetic distances (measured as the sum of distances from the two species to their last common ancestor).

It appears they assumed a universal common ancestor from the start.  And as shown by a paper reported here on 03/17/2006, scientific papers can perpetuate false “microparadigms” by referring to other papers uncritically.
    These worries notwithstanding, what remained was for the team to show a correlation between modularity and phylogeny.  They generated a large circular diagram color-coded with modularity values for the assumed phylogenetic tree of bacteria.  Unfortunately for their thesis, the color values appear random.  To the rescue: the team had lots of explanations for why the anomalies were really not significant.
    There actually is a correlation if you look at it right, they said.  Each exception had a ready explanation.  Horizontal gene transfer, obligate parasitism, unusual environmental factors, a trend downward in modularity as one goes up the tree – there was no shortage of reasons why they found that modularity was only “moderately concordant with organismal phylogeny along the tree of life.”  There is the tree-of-life assumption again.
    Let the disinterested reader evaluate the following claims and caveats in the paper.  Are these valid explanations, or rescuing devices for a theory in crisis?  Keep in mind that the goal of the paper was to establish the claim that all bacteria have evolved from a common ancestor, and the evolutionary tree should be visible in the modularity of their metabolic networks.

1. Overall, our analysis is applied to a large set of 325 reconstructed bacterial metabolic networks (of which 138 appear on the phylogenetic tree), offering insights concerning the forces that have shaped the modularity of metabolic networks since the dawn of bacterial life.
2. Given the moderate level of this overall correlation, it is instructive to examine a few specific cases, where different phylogenetic-modularity similarity patterns emerge.
3. Obviously, habitat variability may also increase as larger classes are examined, so phylogenetic proximity probably involves both genetic and environmental similarities.
4. Other cases, however, may involve substantial variation among strains of the same species…. Such divergence of modularity scores across closely related strains is likely to occur because of the loss of just very few central reactions, fragmenting the metabolic network and consequently altering modularity scores in a considerable manner…. Clearly, such loss of central reactions that affects major metabolic functions is probably detrimental and hence very rare….. Reassuringly, one may note that such variation in modularity among strains is probably not just a result of varying annotation practices that bias the Kyoto Encyclopedia of Genes and Genomes (KEGG) data….
5. In summary, there is an overall rather marked correlation between network size and modularity, but it mainly arises because of the significantly lower modularity scores of small-sized networks.  Interestingly, no significant correlation was observed between bacterial growth rate and modularity… despite the fact that network size is positively correlated with a faster growth rate….
6. It is instructive to examine some of the outliers marked by an asterisk in Fig. 3a; specifically, a few species of Rickettsia and Borrelia have very small networks but high modularity scores.  Although genetically very remote, these species have a shared lifestyle—they are obligate mammalian pathogens that are transmitted by parasitic insects such as fleas or ticks.  This intricate life cycle requires a rapid and efficient shift between two very different environments, which probably dictated the emergence of niche-specific metabolic subsystems, increasing modularity.  This may be an extreme example of the principle laid out by ref. 19, that environmental diversity promotes network modularity.
7. Interestingly, among the host-associated organisms, endosymbionts have miniscule metabolic networks … but these networks are slightly more modular than those of commensals and pathogens … Furthermore, we find that thermophilic bacteria have significantly higher modularity scores than organisms in either mesophilic … or hyperthermophilic … environments, and facultative bacteria have lower modularity scores than aerobic bacteria … (after correcting for multiple hypotheses testing using the Bonferroni correction).  However, the evolutionary forces that have shaped these differences remain unclear.
8. Finally, we note that the genomic fraction of transporters and permeases, which may have been putatively thought to constitute a simple rough correlate of environmental diversity, does not manifest a significant correlation with network modularity.
9. This overall trend, where ancestral modularity scores tend to be higher than those of the descendants, may be attributed to speciation and niche specialization of the organism and to the gradual addition of more peripheral metabolic pathways during evolution.
10. An additional important force that has been assumed to effect the emergence of modularity in metabolic networks is HGT [horizontal gene transfer].  HGT refers to several biological mechanisms by which one organism may transfer genetic material to another organism that is not its descendant and is a major evolutionary force in prokaryotes.

In summary, they concluded that the correlation of modularity to phylogeny is modest at best:

This complex mixture of driving forces reinforces the notion that modularity can be thought of as a product of both the organism’s past evolutionary heritage and its present adaptation to a certain lifestyle and to available niches.  The determination of whether modularity is a converging vs. a genetic trait remains an open challenge.

After this, they unloaded a series of “methodological limitations” that might randomize the modest correlation even further.  They left it to others to see if the correlation would hold up outside the limited scope of their study: “It remains to be seen whether the forces identified here in bacterial metabolic networks do play a similar or a different role in the evolution of modularity in other kinds of biological networks.”  So what, exactly, was demonstrated?

1.  Kreimer, Borenstein, Gophna and Ruppin, “The evolution of modularity in bacterial metabolic networks,” Proceedings of the National Academy of Sciences USA, Published online on May 6, 2008, 10.1073/pnas.0712149105

Every once in awhile we need to take our readers kicking and screaming into the stench of the baloney factory to show them how the Darwin sausage is made.  We know you can only stand it for a few minutes at a time.  This is the garbage that is force-fed to students.  They have no choice; it’s the only thing on the menu.
    We bring you the very best smelly sausage.  This was not cooked up in a corner; it was presented by the National Academy of Sciences, one of the most prestigious scientific societies in the world.  It passed peer review.  No one in the Academy criticized it.  This can be considered representative of the very best the Darwinists have to offer in support of their world view that humans had bacteria ancestors by a chance process with no design.
    There were more rescuing devices in this paper than reasons to believe in evolution.  Even when they assumed evolution and referred to other evolutionary papers, they could only find a modest correlation at best, with whopping outliers and anomalies that had to be explained away.  Worse, they failed to even consider other explanations for the data.  It was DIDO all the way – Darwin in, Darwin out, and DIGO, too: Darwin in, garbage out.  The data were only incidental to the storytelling spree – mere props in the never-ending Darwin drama.
    Did you catch them conjuring up evolutionary “forces”?  We think of forces in science like gravity and electromagnetism, but they redefined the word.  To them, a force is any happenstance that steers the miracle-working potential of evolutionary tinkering.  Did they ever explain how a new environment would generate the necessary random mutations that were supposed to create new, functional metabolic networks?  Never; they merely assumed it would.  Referring to horizontal gene transfer as a source of innovation only pushes the miracle onto another germ.  Playing theoretical hot potato is not a scientific way to explain how complex interactions of highly-specific protein parts came about.  Remember?  They even admitted that tinkering with networks is probably detrimental and extremely rare – but in their view, tinkering is the only available source of innovation.
    At one point they said, “the evolutionary forces that have shaped these differences remain unclear,” but a few paragraphs later they were crowing about “the forces identified here”.  Forces?  What forces?  Let’s see an equation.  There were no forces; just obstacles.  The telephone pole on the sidewalk does not force a bicycle rider to become an airplane pilot.  More likely, it forces him into an opportunity for a concussion.
    Undoubtedly, the Darwin Party Propaganda Mill will add this paper to their mountain of evidence that supports Darwin.  They will argue also that nothing in biology makes sense without evolution.  They will use it to show how much useful science Darwinism is generating.  In truth, the guys in the baloney factory spill their guts and sacrifice their brains into the mix to show their devotion to Charlie.  Maybe that’s why the Good Book warned against eating meat offered to idols.